title: Isolation and bioinformatic analysis of a novel transposable element, ISCbe4, from the hyperthermophilic bacterium, Caldicellulosiruptor bescii.
abstract: Caldicellulosiruptor bescii is an anaerobic thermophilic bacterium of special interest for use in the consolidated bioprocessing of plant biomass to biofuels. In the course of experiments to engineer pyruvate metabolism in C. bescii, we isolated a mutant of C. bescii that contained an insertion in the L-lactate dehydrogenase gene (ldh). PCR amplification and sequencing of the ldh gene from this mutant revealed a 1,609-bp insertion that contained a single open reading frame of 479 amino acids (1,440 bp) annotated as a hypothetical protein with unknown function. The ORF is flanked by an 8-base direct repeat sequence. Bioinformatic analysis indicated that this ORF is part of a novel transposable element, ISCbe4, which is only intact in the genus Caldicellulosiruptor, but has ancient relatives that are present in degraded (and previously unrecognized) forms across many bacterial and archaeal clades.
authors.affiliation: Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
authors.forename: Minseok
authors.initials: M
authors.lastname: Cha
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.forename: Daehwan
authors.initials: D
authors.lastname: Chung
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Janet
authors.initials: J
authors.lastname: Westpheling
mesh_terms: D018533:Biomass; D019295:Computational Biology; D004251:DNA Transposable Elements / Q000235:genetics*; D006094:Gram-Positive Bacteria / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D007770:L-Lactate Dehydrogenase / Q000235:genetics* / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D004251:DNA Transposable Elements; D007770:L-Lactate Dehydrogenase